Our installation of InDesign CS6 was manually activated on our master image, but after we rearm the image and deployed via Citrix XenDesktop 7.6 as a non-persistent VDI, the application requires reactivation. Are there any guidelines as to how we should be installing/configuring it?

I've been a user of InDesign since it began and have provided support for a lot of people. I can't make any sense out of your question. I'm guessing you must be using some non-standard installation process like an enterprise account. The concepts of "rearming the image" and "deploying via CitrixDesktop" are not standard processes. You should probably consult with your Enterprise support team.